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- PDB-9rvu: in situ S. pombe hibernating ribosome after 7 days of glucose dep... -

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Basic information

Entry
Database: PDB / ID: 9rvu
Titlein situ S. pombe hibernating ribosome after 7 days of glucose depletion
Components
  • (Large ribosomal subunit protein ...) x 43
  • (Small ribosomal subunit protein ...) x 32
  • 18S small subunit ribosomal RNA
  • 28S large subunit ribosomal RNA
  • 5.8S large subunit ribosomal RNA
  • 5S large subunit ribosomal RNA
  • Elongation factor 2
  • Eukaryotic translation initiation factor 5A-1
  • Ribosome-associated protein oga1
  • SDO1-like protein C21C3.19
KeywordsRIBOSOME / SNOR / pombe / Yeast / Hibernating / Glucose / Cryo-ET / in-situ
Function / homology
Function and homology information


Peptide chain elongation / Hypusine synthesis from eIF5A-lysine / Synthesis of diphthamide-EEF2 / mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Platelet degranulation / Protein methylation / Protein hydroxylation ...Peptide chain elongation / Hypusine synthesis from eIF5A-lysine / Synthesis of diphthamide-EEF2 / mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Platelet degranulation / Protein methylation / Protein hydroxylation / regulation of cytoplasmic translational initiation in response to stress / RMTs methylate histone arginines / Neutrophil degranulation / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of cell integrity MAPK cascade / ribonuclease MRP complex / positive regulation of conjugation with cellular fusion / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational frameshifting / regulation of cytoplasmic translation / cytoplasmic translational elongation / GCN2-mediated signaling / positive regulation of translational termination / translation termination factor activity / translation activator activity / negative regulation of p38MAPK cascade / cytoplasmic translational termination / ribosome hibernation / positive regulation of translational elongation / preribosome / G-quadruplex DNA binding / tRNA processing / cytosolic large ribosomal subunit assembly / signaling receptor activator activity / negative regulation of translational frameshifting / TOR signaling / ribosomal small subunit binding / translational elongation / ribosomal large subunit export from nucleus / pre-mRNA intronic binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation elongation factor activity / protein-RNA complex assembly / maturation of LSU-rRNA / negative regulation of cytoplasmic translation / protein-membrane adaptor activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of autophagy / rescue of stalled cytosolic ribosome / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of actin cytoskeleton organization / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / negative regulation of gene expression / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / nucleolus / protein-containing complex / RNA binding / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal ...Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Stm1-like, N-terminal / Stm1 / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : / Ribosomal protein L28e / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / : / Ribosomal protein S26e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Translation elongation factor EFTu-like, domain 2 / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / : / Ribosomal protein L10e signature. / Ribosomal protein L6e signature. / Ribosomal protein L44e signature. / 40S Ribosomal protein S10 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Elongation factor Tu domain 2 / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / :
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS10B / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS12A ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS10B / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS12A / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS7A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A / Elongation factor 2 / Large ribosomal subunit protein eL19B / Large ribosomal subunit protein eL21B / Large ribosomal subunit protein uL13A / Ribosome-associated protein oga1 / Small ribosomal subunit protein eS17A / Small ribosomal subunit protein uS4B / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30C / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL18B / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL1B / Large ribosomal subunit protein eL24B / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL6B / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein eS1B / Large ribosomal subunit protein eL36B / Large ribosomal subunit protein eL37B / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL39 / Ubiquitin-ribosomal protein eL40A fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL14A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS12A / Large ribosomal subunit protein uL5A / Small ribosomal subunit protein eS28A / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein uL3A / Large ribosomal subunit protein eL30A / Eukaryotic translation initiation factor 5A-1 / Large ribosomal subunit protein uL15B / Small ribosomal subunit protein eS19A / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS25A / Large ribosomal subunit protein eL32A / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL16A / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL23A / Large ribosomal subunit protein eL18B / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein eS6B / Large ribosomal subunit protein eL43A / Small ribosomal subunit protein eS4C / Small ribosomal subunit protein eS8B / SDO1-like protein C21C3.19 / Large ribosomal subunit protein eL34B / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL15B / Large ribosomal subunit protein eL38A / Large ribosomal subunit protein eL33A / Small ribosomal subunit protein eS26B / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS19B / Small ribosomal subunit protein uS2A
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 3.38 Å
AuthorsRosa, H. / Gluc, M. / Jomaa, A. / Mattei, S.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: To Be Published
Title: A novel eukaryotic ribosome factor promotes translation restart after dormancy
Authors: Gluc, M. / Rosa, H. / Bozko, M. / Prince, C.R. / Turner, L.A. / Peskova, Y. / Feaga, H.A. / Gould, K.L. / Mattei, S. / Jomaa, A.
History
DepositionJul 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Part number: 2 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 18S small subunit ribosomal RNA
AD: Small ribosomal subunit protein uS2A
AE: Small ribosomal subunit protein eS1B
AF: Small ribosomal subunit protein uS5
AG: Small ribosomal subunit protein uS3
AH: Small ribosomal subunit protein eS4C
AI: Small ribosomal subunit protein uS7A
AJ: Small ribosomal subunit protein eS6B
AK: Small ribosomal subunit protein eS7
AL: Small ribosomal subunit protein eS8B
AM: Small ribosomal subunit protein uS4B
AN: Small ribosomal subunit protein eS10B
AO: Small ribosomal subunit protein uS17A
AP: Small ribosomal subunit protein eS12A
AQ: Small ribosomal subunit protein uS15
AR: Small ribosomal subunit protein uS11A
AS: Small ribosomal subunit protein uS19B
AT: Small ribosomal subunit protein uS9A
AU: Small ribosomal subunit protein eS17A
AV: Small ribosomal subunit protein uS13A
AW: Small ribosomal subunit protein eS19A
Aa: Small ribosomal subunit protein uS10
Ab: Small ribosomal subunit protein eS21
Ac: Small ribosomal subunit protein uS8A
Ad: Small ribosomal subunit protein uS12A
Ae: Small ribosomal subunit protein eS24A
Af: Small ribosomal subunit protein eS25A
Ag: Small ribosomal subunit protein eS26B
Ah: Small ribosomal subunit protein eS27
Ai: Small ribosomal subunit protein eS28A
Aj: Small ribosomal subunit protein uS14
Ak: Small ribosomal subunit protein eS30A
Am: Small ribosomal subunit protein RACK1
B0: Large ribosomal subunit protein eL42
B1: Large ribosomal subunit protein eL43A
B2: 28S large subunit ribosomal RNA
B3: 5S large subunit ribosomal RNA
B4: 5.8S large subunit ribosomal RNA
BN: Large ribosomal subunit protein uL2A
BO: Large ribosomal subunit protein uL3A
BP: Large ribosomal subunit protein uL4A
BQ: Large ribosomal subunit protein uL18B
BR: Large ribosomal subunit protein eL6
BS: Large ribosomal subunit protein uL30C
BT: Large ribosomal subunit protein eL8
BV: Large ribosomal subunit protein uL16A
BW: Large ribosomal subunit protein uL5A
BX: Large ribosomal subunit protein eL13
BY: Large ribosomal subunit protein eL14
BZ: Large ribosomal subunit protein eL15B
Ba: Large ribosomal subunit protein uL13A
Bc: Large ribosomal subunit protein eL18B
Bd: Large ribosomal subunit protein eL19B
Be: Large ribosomal subunit protein eL20A
Bf: Large ribosomal subunit protein eL21B
Bg: Large ribosomal subunit protein eL22
Bh: Large ribosomal subunit protein uL14A
Bi: Large ribosomal subunit protein eL24B
Bj: Large ribosomal subunit protein uL23A
Bk: Large ribosomal subunit protein uL24
Bl: Large ribosomal subunit protein eL27A
Bm: Large ribosomal subunit protein uL15B
Bn: Large ribosomal subunit protein eL29
Bo: Large ribosomal subunit protein eL30A
Bp: Large ribosomal subunit protein eL31
Bq: Large ribosomal subunit protein eL32A
Br: Large ribosomal subunit protein eL33A
Bs: Large ribosomal subunit protein eL34B
Bt: Large ribosomal subunit protein uL29
Bu: Large ribosomal subunit protein eL36B
Bv: Large ribosomal subunit protein eL37B
Bw: Large ribosomal subunit protein eL38A
Bx: Large ribosomal subunit protein eL39
By: Large ribosomal subunit protein eL28
H1: Ribosome-associated protein oga1
HE: Elongation factor 2
HL: Large ribosomal subunit protein uL1B
HS: SDO1-like protein C21C3.19
HI: Eukaryotic translation initiation factor 5A-1
BA: Large ribosomal subunit protein eL40A
BU: Large ribosomal subunit protein uL6B
Bb: Large ribosomal subunit protein uL22A
A: Large ribosomal subunit protein uL22A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,370,70189
Polymers3,370,30983
Non-polymers3926
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 4 molecules AAB2B3B4

#1: RNA chain 18S small subunit ribosomal RNA


Mass: 593528.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#36: RNA chain 28S large subunit ribosomal RNA


Mass: 1129812.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#37: RNA chain 5S large subunit ribosomal RNA


Mass: 78518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 157310380
#38: RNA chain 5.8S large subunit ribosomal RNA


Mass: 52880.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 1607200062

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Small ribosomal subunit protein ... , 32 types, 32 molecules ADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAaAbAcAdAeAfAgAhAiAjAkAm

#2: Protein Small ribosomal subunit protein uS2A / 40S ribosomal protein S0-A


Mass: 31794.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9Y7L8
#3: Protein Small ribosomal subunit protein eS1B / 40S ribosomal protein S1-B / S3aE-B


Mass: 28574.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94438
#4: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 27681.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74892
#5: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 27594.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O60128
#6: Protein Small ribosomal subunit protein eS4C / 40S ribosomal protein S4-C


Mass: 29735.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P4W9
#7: Protein Small ribosomal subunit protein uS7A / 40S ribosomal protein S5-A


Mass: 22257.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14277
#8: Protein Small ribosomal subunit protein eS6B / 40S ribosomal protein S6-B


Mass: 27537.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9C0Z7
#9: Protein Small ribosomal subunit protein eS7 / 40S ribosomal protein S7


Mass: 21987.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10101
#10: Protein Small ribosomal subunit protein eS8B / 40S ribosomal protein S8-B


Mass: 22614.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7B2
#11: Protein Small ribosomal subunit protein uS4B / 40S ribosomal protein S9-B


Mass: 22290.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59675
#12: Protein Small ribosomal subunit protein eS10B / 40S ribosomal protein S10-B


Mass: 16470.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13614
#13: Protein Small ribosomal subunit protein uS17A / 40S ribosomal protein S11-A


Mass: 17535.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT73
#14: Protein Small ribosomal subunit protein eS12A / 40S ribosomal protein S12-A


Mass: 15632.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14062
#15: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 16985.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P28189
#16: Protein Small ribosomal subunit protein uS11A / 40S ribosomal protein S14-A


Mass: 14723.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT56
#17: Protein Small ribosomal subunit protein uS19B / 40S ribosomal protein S15-B


Mass: 17667.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTQ6
#18: Protein Small ribosomal subunit protein uS9A / 40S ribosomal protein S16-A


Mass: 15424.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT64
#19: Protein Small ribosomal subunit protein eS17A / 40S ribosomal protein S17-A


Mass: 15544.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42984
#20: Protein Small ribosomal subunit protein uS13A / 40S ribosomal protein S18-A


Mass: 17470.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT66
#21: Protein Small ribosomal subunit protein eS19A / 40S ribosomal protein S19-A / S16-A


Mass: 16178.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P58234
#22: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13569.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74893
#23: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21 / S28


Mass: 9627.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05764
#24: Protein Small ribosomal subunit protein uS8A / 40S ribosomal protein S22-A


Mass: 14785.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT58
#25: Protein Small ribosomal subunit protein uS12A / 40S ribosomal protein S23-A


Mass: 15691.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT75
#26: Protein Small ribosomal subunit protein eS24A / 40S ribosomal protein S24-A


Mass: 15506.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13784
#27: Protein Small ribosomal subunit protein eS25A / 40S ribosomal protein S25-A / S31-A


Mass: 9979.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79009
#28: Protein Small ribosomal subunit protein eS26B / 40S ribosomal protein S26-B


Mass: 13895.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTG4
#29: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27


Mass: 9185.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74330
#30: Protein Small ribosomal subunit protein eS28A / 40S ribosomal protein S28-A / S33


Mass: 7678.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT79
#31: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6672.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74329
#32: Protein Small ribosomal subunit protein eS30A / 40S ribosomal protein S30-A


Mass: 6928.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT62
#33: Protein Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-like protein / Receptor of activated protein kinase C


Mass: 34887.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10281

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Large ribosomal subunit protein ... , 43 types, 43 molecules B0B1BNBOBPBQBRBSBTBVBWBXBYBZBaBcBdBeBfBgBhBiBjBkBlBmBnBoBpBq...

#34: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L42


Mass: 12239.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTI8
#35: Protein Large ribosomal subunit protein eL43A / 60S ribosomal protein L43-A / L37A


Mass: 10444.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9HGL8
#39: Protein Large ribosomal subunit protein uL2A / 60S ribosomal protein L2-A / K37 / K5 / KD4


Mass: 27151.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT70
#40: Protein Large ribosomal subunit protein uL3A / 60S ribosomal protein L3-A / SP-L1


Mass: 43889.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P40372
#41: Protein Large ribosomal subunit protein uL4A / 60S ribosomal protein L4-A / L2


Mass: 39839.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P35679
#42: Protein Large ribosomal subunit protein uL18B / 60S ribosomal protein L5-B


Mass: 33538.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74306
#43: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6


Mass: 21285.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79071
#44: Protein Large ribosomal subunit protein uL30C / 60S ribosomal protein L7-C


Mass: 28780.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O60143
#45: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L8 / L4 / L7A


Mass: 28659.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13672
#46: Protein Large ribosomal subunit protein uL16A / 60S ribosomal protein L10-A / QM protein homolog / SpQM


Mass: 25421.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09127
#47: Protein Large ribosomal subunit protein uL5A / 60S ribosomal protein L11-A


Mass: 19928.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT77
#48: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13


Mass: 23578.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74175
#49: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 15241.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94238
#50: Protein Large ribosomal subunit protein eL15B / 60S ribosomal protein L15-B / SP-L12


Mass: 23878.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9US22
#51: Protein Large ribosomal subunit protein uL13A / 60S ribosomal protein L16-A


Mass: 22050.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42848
#52: Protein Large ribosomal subunit protein eL18B / 60S ribosomal protein L18-B


Mass: 21234.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q8TFH1
#53: Protein Large ribosomal subunit protein eL19B / 60S ribosomal protein L19-B


Mass: 22813.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42699
#54: Protein Large ribosomal subunit protein eL20A / 60S ribosomal protein L20-A / SP-L17


Mass: 20642.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT68
#55: Protein Large ribosomal subunit protein eL21B / 60S ribosomal protein L21-B


Mass: 18390.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42706
#56: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 13344.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09668
#57: Protein Large ribosomal subunit protein uL14A / 60S ribosomal protein L23-A


Mass: 14905.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT60
#58: Protein Large ribosomal subunit protein eL24B / 60S ribosomal protein L24-B


Mass: 16957.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74884
#59: Protein Large ribosomal subunit protein uL23A / 60S ribosomal protein L25-A


Mass: 15870.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10330
#60: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 14375.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P78946
#61: Protein Large ribosomal subunit protein eL27A / 60S ribosomal protein L27-A


Mass: 15421.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14388
#62: Protein Large ribosomal subunit protein uL15B / 60S ribosomal protein L28-B


Mass: 16723.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P57728
#63: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / L43


Mass: 7224.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q92366
#64: Protein Large ribosomal subunit protein eL30A / 60S ribosomal protein L30-1 / L32


Mass: 11610.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P52808
#65: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 13290.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9URX6
#66: Protein Large ribosomal subunit protein eL32A / 60S ribosomal protein L32-A


Mass: 14491.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79015
#67: Protein Large ribosomal subunit protein eL33A / 60S ribosomal protein L33-A / L37A


Mass: 12212.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USX4
#68: Protein Large ribosomal subunit protein eL34B / 60S ribosomal protein L34-2 / 60S ribosomal protein L34-B


Mass: 12828.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9URT8
#69: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14333.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74904
#70: Protein Large ribosomal subunit protein eL36B / 60S ribosomal protein L36-B


Mass: 11287.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94658
#71: Protein Large ribosomal subunit protein eL37B / 60S ribosomal protein L37-B / SP-L27


Mass: 10112.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05733
#72: Protein Large ribosomal subunit protein eL38A / 60S ribosomal protein L38-1


Mass: 8511.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USR7
#73: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39 / SP-L36


Mass: 6326.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05767
#74: Protein Large ribosomal subunit protein eL28 / Probable 60S ribosomal protein L28e


Mass: 14781.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14069
#77: Protein Large ribosomal subunit protein uL1B / 60S ribosomal protein L1-B / L10a


Mass: 23959.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74836
#80: Protein Large ribosomal subunit protein eL40A / 60S ribosomal protein L40 / CEP52


Mass: 5960.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CH06
#81: Protein Large ribosomal subunit protein uL6B / 60S ribosomal protein L9-B


Mass: 21413.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74905
#82: Protein Large ribosomal subunit protein uL22A / 60S ribosomal protein L17-A


Mass: 20854.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14339
#83: Protein/peptide Large ribosomal subunit protein uL22A / 60S ribosomal protein L17-A


Mass: 2130.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14339

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Protein , 4 types, 4 molecules H1HEHSHI

#75: Protein Ribosome-associated protein oga1 / Ortholog of G4-associated protein 1 / Ribosome clamping factor oga1


Mass: 31007.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42914
#76: Protein Elongation factor 2 / EF-2


Mass: 93344.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14460
#78: Protein SDO1-like protein C21C3.19


Mass: 11909.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7K6
#79: Protein Eukaryotic translation initiation factor 5A-1 / eIF-5A-1


Mass: 17260.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P56289

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Non-polymers , 1 types, 6 molecules

#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: In situ cryo-ET Hibernating Ribosome from S. pombe under 7-day glucose depletion conditions
Type: RIBOSOME
Details: Full hibernating ribosome (Large and Small Subunits) with eEF2, eIF5a (with hypusination), SNOR (SBDS-domain containing hibernation factor), and Stm1.
Entity ID: #1-#83 / Source: NATURAL
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Objective Aperture 70 um
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.4 e/Å2 / Avg electron dose per subtomogram: 140 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails
1Warp2.0.0dev36volume selectionWarpTools
2PHENIX1.21.2_5419model refinement
5Warp2.0.0dev36CTF correctionWarpTools
13Warp2.0.0dev363D reconstructionMTools
CTF correctionDetails: 3D CTF Estimation done in Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88206 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 715 / Num. of volumes extracted: 95485
RefinementHighest resolution: 3.38 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002224643
ELECTRON MICROSCOPYf_angle_d0.397328727
ELECTRON MICROSCOPYf_dihedral_angle_d20.96189031
ELECTRON MICROSCOPYf_chiral_restr0.02740960
ELECTRON MICROSCOPYf_plane_restr0.00322399

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